@sjcrh/proteinpaint-client 2.196.0 → 2.198.0

package/dist/grin2-V36KLEBU.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/grin2/model/GRIN2Model.ts", "../plots/grin2/viewModel/GRIN2ViewModel.ts", "../plots/manhattan/manhattan.ts", "../plots/grin2/view/GRIN2ResultsView.ts", "../plots/grin2/settings/defaults.ts", "../plots/grin2/view/GRIN2ControlsView.ts", "../plots/grin2/grin2.ts"],
+  "sourcesContent": ["import type { GRIN2RequestData, GRIN2Response } from '../GRIN2Types'\n\n/** Server-interaction layer for the GRIN2 plot.\n *  Wraps the vocabApi getter so the controller stays free of fetch concerns. */\nexport class GRIN2Model {\n\tprivate vocabApi: any\n\n\tconstructor(vocabApi: any) {\n\t\tthis.vocabApi = vocabApi\n\t}\n\n\tasync fetchGrin2Data(requestData: GRIN2RequestData, signal?: AbortSignal): Promise<GRIN2Response> {\n\t\treturn this.vocabApi.getGrin2Data(requestData, signal)\n\t}\n}\n", "import { dt2lesion } from '#shared/common.js'\nimport type { GRIN2Response, GRIN2ViewData, DtUsage } from '../GRIN2Types'\n\n/** Transforms a GRIN2 server response into display-ready ViewData.\n *  All conditional shaping (significance circles, header text)\n *  lives here so the View stays a thin renderer. */\nexport class GRIN2ViewModel {\n\tviewData: GRIN2ViewData\n\n\tconstructor(response: GRIN2Response, manhattanSettings: any, dtUsage: DtUsage) {\n\t\tthis.viewData = {\n\t\t\tmanhattan: response.pngImg ? { plotData: response, settings: manhattanSettings } : null,\n\t\t\ttopGenes: this.buildTopGenes(response, manhattanSettings, dtUsage),\n\t\t\tstatsSections: response.stats?.lst || []\n\t\t}\n\t}\n\n\tprivate buildTopGenes(response: GRIN2Response, manhattanSettings: any, dtUsage: DtUsage): GRIN2ViewData['topGenes'] {\n\t\tif (!response.topGeneTable || !response.stats?.lst) return null\n\n\t\t// \"showing N of M\": N = genes actually in the table, M = total genes GRIN tested. Look up the\n\t\t// total-genes cell by label rather than positional index (rows[0]) so reordering the Summary\n\t\t// rows can't silently turn this into a wrong/sample count.\n\t\tconst totalGenes = response.stats.lst[0].rows.find((r: any) => r[0] === 'Total Genes')?.[1] ?? '?'\n\t\tconst headerText = `Top Genes (showing ${response.topGeneTable.rows.length.toLocaleString()} of ${totalGenes})`\n\n\t\tconst qValueEntries = this.buildQValueEntries(response.topGeneTable.columns, dtUsage)\n\t\tconst lesionTypeCircleCache = this.buildCircleCache(manhattanSettings.lesionTypeColors)\n\t\tconst qValueThreshold = manhattanSettings.qValueThreshold\n\n\t\tconst rows = response.topGeneTable.rows.map((row: any) => {\n\t\t\tconst circles = qValueEntries\n\t\t\t\t.filter(({ colIndex }) => {\n\t\t\t\t\tconst qValue = row[colIndex]?.value\n\t\t\t\t\treturn typeof qValue === 'number' && qValue < qValueThreshold\n\t\t\t\t})\n\t\t\t\t.map(({ type }) => lesionTypeCircleCache.get(type)!)\n\t\t\treturn [{ value: '', html: circles.join('') }, ...row]\n\t\t})\n\n\t\treturn {\n\t\t\theaderText,\n\t\t\tcolumns: [{ label: '', width: '20px' }, ...response.topGeneTable.columns],\n\t\t\trows,\n\t\t\tdataItems: response.topGeneTable.rows\n\t\t}\n\t}\n\n\tprivate buildQValueEntries(columns: { label: string }[], dtUsage: DtUsage): { colIndex: number; type: string }[] {\n\t\tconst dtMapping: Record<string, { col: string; type: string }[]> = {}\n\t\tObject.entries(dt2lesion).forEach(([dt, cfg]: [string, any]) => {\n\t\t\tdtMapping[dt] = cfg.lesionTypes.map((lt: any) => ({\n\t\t\t\tcol: `Q-value (${lt.name})`,\n\t\t\t\ttype: lt.lesionType\n\t\t\t}))\n\t\t})\n\n\t\tconst entries: { colIndex: number; type: string }[] = []\n\t\tObject.entries(dtUsage).forEach(([key, info]: [string, any]) => {\n\t\t\t// dtUsage values may be either { checked: bool } objects or bare booleans depending on call site\n\t\t\tconst isChecked = typeof info === 'object' ? info?.checked : !!info\n\t\t\tif (isChecked && dtMapping[key]) {\n\t\t\t\tdtMapping[key].forEach(({ col, type }) => {\n\t\t\t\t\tconst colIndex = columns.findIndex(c => c.label === col)\n\t\t\t\t\tif (colIndex !== -1) entries.push({ colIndex, type })\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t\treturn entries\n\t}\n\n\tprivate buildCircleCache(lesionTypeColors: Record<string, string>): Map<string, string> {\n\t\treturn new Map(\n\t\t\tObject.entries(lesionTypeColors).map(([type, color]) => [\n\t\t\t\ttype,\n\t\t\t\t`<span style=\"display:inline-block;width:8px;height:8px;border-radius:50%;background-color:${color};margin-right:3px;\"></span>`\n\t\t\t])\n\t\t)\n\t}\n}\n", "import { scaleLinear } from 'd3-scale'\nimport * as d3axis from 'd3-axis'\nimport { select } from 'd3-selection'\nimport {\n\tMenu,\n\ticons,\n\taxisstyle,\n\ttable2col,\n\tshowResultsTable,\n\tcreateLollipopFromGene,\n\tDataPointInteractions\n} from '#dom'\nimport { to_svg } from '#src/client'\nimport type { ManhattanPoint } from './manhattanTypes'\n\n/**\n * Creates an interactive Manhattan plot on top of a PNG background plot image.\n *\n * @param {Object} div - div element to contain the plot\n * @param {Object} data - Plot data\n * @param {Object} settings - Display configuration options:\n *   @param {number} [settings.plotWidth=500] - Plot area width\n *   @param {number} [settings.plotHeight=200] - Plot area height\n *   @param {boolean} [settings.showLegend=true] - Whether to display legend\n *   @param {boolean} [settings.showDownload=true] - Whether to show download button\n *   @param {boolean} [settings.showInteractiveDots=true] - Whether to show hoverable data points\n *   @param {number} [settings.yAxisX=70] - Y-axis positioning\n *   @param {number} [settings.yAxisSpace=40] - Space between Y-axis and plot\n *   @param {number} [settings.yAxisY=40] - Top margin\n *   @param {number} [settings.fontSize=12] - Base font size\n *   @param {number} [settings.pngDotRadius=2] - Radius of dots in PNG plot\n *   @param {number} [settings.legendItemWidth=80] - Horizontal space per legend item\n *   @param {number} [settings.legendDotRadius=3] - Size of legend dots\n *   @param {number} [settings.legendRightOffset=15] - Offset from right edge\n *   @param {number} [settings.legendTextOffset=12] - Distance between dot and text\n *   @param {number} [settings.legendVerticalOffset=4] - Vertical offset for legend items\n *   @param {number} [settings.legendFontSize=12] - Font size for legend text\n *   @param {number} [settings.interactiveDotRadius=2] - Radius of interactive dots\n *   @param {number} [settings.xAxisLabelPad=20] - Amount of padding we give for x-axis title padding\n *   @param {number} [settings.interactiveDotStrokeWidth=1] - Stroke width for interactive dots\n *   @param {string} [settings.axisColor='#545454'] - Color for y-axis\n *   @param {boolean} [settings.showYAxisLine=true] - Whether to show y-axis line\n *   @param {number} [settings.interactiveDotsCap=5000] - Interactive dots cap\n *   @param {number} [settings.maxTooltipGenes=5] - Maximum number of genes to show in tooltip\n * @param {Object} [app] - Optional app context for dispatching events\n *\n *\n * @description\n * Renders a genomic Manhattan plot by overlaying interactive elements on the base PNG plot image.\n * Features include chromosome labels, legend, hoverable data points with tooltips,\n * and proper axis scaling. The plot combines a static PNG plot image of all points with dynamic SVG elements\n * including axes, labels, legend, and top genes (represented as interactive dots) for detailed information on hover.\n */\n\nexport function plotManhattan(div: any, data: any, settings: any, app?: any) {\n\t// Get our settings\n\tsettings = {\n\t\t...settings\n\t}\n\n\t// Check size of interactive data\n\tlet interactivePoints = data.plotData.points\n\tif (data.plotData.points.length > settings.interactiveDotsCap) {\n\t\t// Sort points by y value (-log10(q-value)) descending and take top N up to interactiveDotsCap\n\t\tinteractivePoints = data.plotData.points.sort((a: any, b: any) => b.y - a.y).slice(0, settings.interactiveDotsCap)\n\t}\n\n\t// Set the  positioning up for download button to work properly\n\tdiv.style('position', 'relative')\n\n\t// Hover tooltip menu \u2014 DataPointInteractions writes into this on hover.\n\tconst geneTip = new Menu({ padding: '' })\n\n\tconst svg = div\n\t\t.append('svg')\n\t\t.attr('data-testid', 'sjpp-manhattan')\n\t\t.attr('width', settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace)\n\t\t.attr('height', settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4) // Extra space for x-axis labels, legend, and title\n\n\t// Add y-axis\n\t// yPlot       \u2192 full padded scale, aligns exactly with PNG coordinates\n\t// yAxisScale  \u2192 trimmed scale for axis labels, ignores PNG padding\n\t// --- Y-Axis Setup ---\n\t// This section builds two linked scales:\n\t//\n\t//   1) yPlot       \u2192 full PNG-aligned scale (includes padding added by Rust)\n\t//   2) yAxisScale  \u2192 visual axis scale (no padding; shows only real data values)\n\t//\n\t// The reason for two scales is that the PNG image itself was rendered\n\t// with top/bottom padding for dot radius. We need one scale to stay\n\t// pixel-perfect with the PNG (for dots, overlays, etc.), and another\n\t// scale to make the visible y-axis line up only with the *real* data region.\n\n\t// 1) yPlot: true positioning scale used for all pixel-aligned elements\n\t//    - Domain = padded range from Rust (includes buffer above/below real data)\n\t//    - Range  = full PNG pixel height (0 is top, png_height is bottom)\n\tconst yPlot = scaleLinear()\n\t\t.domain([data.plotData.y_min, data.plotData.y_max]) // padded domain from Rust\n\t\t.range([settings.plotHeight + 2 * settings.pngDotRadius, 0]) // full PNG height\n\n\t// 2) yAxisScale: used only for the visible axis labels/ticks\n\t//    - Domain = true data values (no padding)\n\t//    - Range  = subset of pixel space between yPlot(0) and yPlot(realMax [data.plotData.y_max - data.plotData.png_dot_radius])\n\t//               so the axis sits entirely within the real data area\n\tconst yAxisScale = scaleLinear()\n\t\t.domain([0, data.plotData.y_max - settings.pngDotRadius])\n\t\t.range([yPlot(0), yPlot(data.plotData.y_max - settings.pngDotRadius)])\n\n\t// Axis group\n\tconst axisG = svg\n\t\t.append('g')\n\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace - settings.yAxisPad},${settings.yAxisY})`)\n\n\taxisG.call(\n\t\td3axis.axisLeft(yAxisScale).tickSizeOuter(0) // removes top/bottom cap lines for clean look\n\t)\n\n\taxisstyle({\n\t\taxis: axisG,\n\t\tcolor: settings.axisColor,\n\t\tfontsize: settings.fontSize + 2,\n\t\tshowline: settings.showYAxisLine\n\t})\n\n\t// Add y-axis label\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', -((settings.plotHeight + 2 * settings.pngDotRadius) / 2) - settings.yAxisY)\n\t\t.attr('y', settings.yAxisX / 2)\n\t\t.attr('transform', 'rotate(-90)')\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', `${settings.fontSize + 4}px`)\n\t\t.attr('fill', 'black')\n\t\t.text(data.plotData.has_capped_points ? '-log\u2081\u2080(q-value) [capped]' : '-log\u2081\u2080(q-value)')\n\n\t// Add png image\n\tsvg\n\t\t.append('image')\n\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`)\n\t\t.attr('width', settings.plotWidth + 2 * settings.pngDotRadius)\n\t\t.attr('height', settings.plotHeight + 2 * settings.pngDotRadius)\n\t\t.attr('href', `data:image/png;base64,${data.pngImg || data.png}`)\n\n\t// Create scales for positioning elements\n\tconst xScale = scaleLinear()\n\t\t.domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer])\n\t\t.range([0, settings.plotWidth + 2 * settings.pngDotRadius])\n\n\t// Add interactive dots layer\n\tif (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {\n\t\t// Hover-ring layer \u2014 `pointer-events: none` so rings never intercept clicks.\n\t\tconst hoverLayer = svg\n\t\t\t.append('g')\n\t\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`)\n\t\t\t.style('pointer-events', 'none')\n\n\t\t// Cover as a sibling HTML div positioned over the plot area \u2014 avoids\n\t\t// the mouse-event quirks of nesting inside SVG.\n\t\tconst cover = select(svg.node().parentNode as HTMLElement)\n\t\t\t.append('div')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('left', `${settings.yAxisX + settings.yAxisSpace}px`)\n\t\t\t.style('top', `${settings.yAxisY}px`)\n\t\t\t.style('width', `${settings.plotWidth + 2 * settings.pngDotRadius}px`)\n\t\t\t.style('height', `${settings.plotHeight + 2 * settings.pngDotRadius}px`)\n\t\t\t.style('pointer-events', 'all')\n\n\t\t// Circle as an SVG path so it flows through the generic `drawHoverShapes`.\n\t\tconst circlePath = (r: number) => `M${r},0 A${r},${r} 0 1,1 ${-r},0 A${r},${r} 0 1,1 ${r},0 Z`\n\n\t\tconst interactions = new DataPointInteractions<ManhattanPoint>({\n\t\t\tcover,\n\t\t\thoverLayer,\n\t\t\thoverTip: geneTip,\n\t\t\tpoints: interactivePoints,\n\t\t\tgetX: d => d.pixel_x,\n\t\t\tgetY: d => d.pixel_y,\n\t\t\thitRadius: settings.pngDotRadius + 3,\n\t\t\ttoHoverSpec: d => ({\n\t\t\t\tpath: circlePath(settings.pngDotRadius),\n\t\t\t\ttransform: `translate(${d.pixel_x},${d.pixel_y})`,\n\t\t\t\tfill: 'none',\n\t\t\t\tstroke: 'black',\n\t\t\t\tstrokeWidth: settings.interactiveDotStrokeWidth\n\t\t\t}),\n\t\t\tmaxTooltipRows: settings.maxTooltipGenes,\n\t\t\titemNoun: 'gene',\n\t\t\trenderSingleHoverTooltip: (d, container) => {\n\t\t\t\tconst table = table2col({ holder: container.append('div'), margin: '10px' })\n\t\t\t\ttable.addRow('Gene', d.gene)\n\t\t\t\ttable.addRow('Position', `${d.chrom}:${d.start}-${d.end}`)\n\t\t\t\tconst [t1, t2] = table.addRow()\n\t\t\t\tt1.text('Type')\n\t\t\t\tt2.html(`<span style=\"color:${d.color}\">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`)\n\t\t\t\ttable.addRow('Q-value', d.q_value.toPrecision(3))\n\t\t\t\ttable.addRow('Subject count', d.nsubj)\n\t\t\t},\n\t\t\tbuildMultiHitTableData: dots => ({\n\t\t\t\tcolumns: [\n\t\t\t\t\t{ label: 'Gene' },\n\t\t\t\t\t{ label: 'Position' },\n\t\t\t\t\t{ label: 'Type' },\n\t\t\t\t\t{ label: 'Q-value', sortable: true },\n\t\t\t\t\t{ label: 'Subject count', sortable: true }\n\t\t\t\t],\n\t\t\t\trows: dots.map(d => [\n\t\t\t\t\t{ value: d.gene },\n\t\t\t\t\t{ value: `${d.chrom}:${d.start}-${d.end}` },\n\t\t\t\t\t{\n\t\t\t\t\t\thtml: `<span style=\"color:${d.color}\">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`\n\t\t\t\t\t},\n\t\t\t\t\t{ value: d.q_value.toPrecision(3) },\n\t\t\t\t\t{ value: d.nsubj }\n\t\t\t\t])\n\t\t\t}),\n\t\t\t// Manhattan single-click goes straight to a lollipop launch \u2014 no menu.\n\t\t\t// Release hover-suppression immediately so the cursor's next move re-engages.\n\t\t\tonSingleClick: (d, _event, ctx) => {\n\t\t\t\tctx.dismiss()\n\t\t\t\tif (app) createLollipopFromGene(d.gene, app)\n\t\t\t},\n\t\t\t// Manhattan multi-click shows showResultsTable directly with `app + clickMenu`\n\t\t\t// so the table renders inline Matrix/Lollipop buttons. Reuses the module's\n\t\t\t// clickMenu so its onHide cleanup (clear flag, clear hover) fires on dismiss.\n\t\t\t// Content is built BEFORE show2 so Menu can measure the populated rect for\n\t\t\t// its right-edge clamp \u2014 otherwise the wide table is placed at cursor+offsetX\n\t\t\t// and extends off the right edge of the viewport.\n\t\t\tonMultiClick: (dots, event, ctx) => {\n\t\t\t\tif (!app) {\n\t\t\t\t\tctx.dismiss()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tctx.clickMenu.clear()\n\t\t\t\tconst holder = ctx.clickMenu.d.append('div').style('margin', '10px')\n\t\t\t\tshowResultsTable({ tableDiv: holder, hits: dots, app, clickMenu: ctx.clickMenu })\n\t\t\t\tctx.clickMenu.show2(event.clientX, event.clientY)\n\t\t\t}\n\t\t})\n\n\t\tinteractions.attach()\n\t}\n\n\t// Add chromosome labels\n\tif (data.plotData.chrom_data) {\n\t\tconst chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + 10\n\n\t\tObject.entries(data.plotData.chrom_data).forEach(([chrom, chromData]: [string, any]) => {\n\t\t\tconst chromLabel = chrom.replace('chr', '')\n\n\t\t\t// Skip chrM\n\t\t\tif (chromLabel === 'M') return\n\n\t\t\t// Calculate center position for label\n\t\t\tconst centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center)\n\n\t\t\t// Append chromosome label\n\t\t\tsvg\n\t\t\t\t.append('text')\n\t\t\t\t.attr('x', centerPos)\n\t\t\t\t.attr('y', chromLabelY)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('font-size', `${settings.fontSize + 2}px`)\n\t\t\t\t.text(chromLabel)\n\t\t})\n\t}\n\n\t// Add x-axis label\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) / 2)\n\t\t.attr('y', settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + settings.xAxisLabelPad)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', `${settings.fontSize + 4}px`)\n\t\t.attr('fill', 'black')\n\t\t.text('Chromosomes')\n\n\t// Add title\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', settings.yAxisX + settings.yAxisSpace)\n\t\t.attr('y', settings.yAxisY / 2)\n\t\t.attr('font-weight', 'bold')\n\t\t.attr('font-size', `${settings.fontSize + 2}px`)\n\t\t.text('Manhattan Plot')\n\n\tif (settings.showDownload) {\n\t\tconst downloadDiv = div\n\t\t\t.append('div')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('top', '5px')\n\t\t\t.style('left', `${settings.yAxisX + settings.yAxisSpace + 108}px`)\n\n\t\ticons['download'](downloadDiv, {\n\t\t\twidth: 16,\n\t\t\theight: 16,\n\t\t\ttitle: 'Download Manhattan plot',\n\t\t\thandler: () => {\n\t\t\t\t// Clone the SVG to avoid modifying the displayed version\n\t\t\t\tconst svgNode = svg.node() as SVGSVGElement\n\t\t\t\tconst clone = svgNode.cloneNode(true) as SVGSVGElement\n\n\t\t\t\t// Get the bounding box of all content\n\t\t\t\tconst bbox = svgNode.getBBox()\n\n\t\t\t\t// Set the clone's dimensions to match the full content\n\t\t\t\tclone.setAttribute('width', bbox.width.toString())\n\t\t\t\tclone.setAttribute('height', bbox.height.toString())\n\t\t\t\tclone.setAttribute('viewBox', `${bbox.x} ${bbox.y} ${bbox.width} ${bbox.height}`)\n\n\t\t\t\tto_svg(clone, `manhattan_plot_${new Date().toISOString().replace(/[:.]/g, '-').slice(0, -5)}`, {\n\t\t\t\t\tapply_dom_styles: true\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\t// Generate legend data\n\tconst mutationTypes = [...new Set(data.plotData.points.map((p: any) => p.type))]\n\tconst legendData = mutationTypes.map(type => {\n\t\tconst point = data.plotData.points.find((p: any) => p.type === type)\n\t\treturn {\n\t\t\ttype: String(type).charAt(0).toUpperCase() + String(type).slice(1),\n\t\t\tcolor: point?.color\n\t\t}\n\t})\n\n\t// Add legend\n\tif (settings.showLegend && legendData.length > 0) {\n\t\tconst legendY = settings.yAxisY / 2\n\t\tconst totalWidth = legendData.length * settings.legendItemWidth\n\t\tconst legendX =\n\t\t\tsettings.yAxisX +\n\t\t\tsettings.yAxisSpace +\n\t\t\t(settings.plotWidth + 2 * settings.pngDotRadius) -\n\t\t\ttotalWidth -\n\t\t\tsettings.legendRightOffset\n\n\t\tlegendData.forEach((item, i) => {\n\t\t\tconst x = legendX + i * settings.legendItemWidth\n\n\t\t\t// Legend dot\n\t\t\tsvg\n\t\t\t\t.append('circle')\n\t\t\t\t.attr('cx', x + 8)\n\t\t\t\t.attr('cy', legendY)\n\t\t\t\t.attr('r', settings.legendDotRadius)\n\t\t\t\t.attr('fill', item.color)\n\n\t\t\t// Legend text\n\t\t\tsvg\n\t\t\t\t.append('text')\n\t\t\t\t.attr('x', x + 8 + settings.legendTextOffset)\n\t\t\t\t.attr('y', legendY + settings.legendVerticalOffset)\n\t\t\t\t.attr('font-size', `${settings.legendFontSize + 2}px`)\n\t\t\t\t.text(item.type)\n\t\t})\n\t}\n}\n", "import { table2col, showResultsTable } from '#dom'\nimport { plotManhattan } from '#plots/manhattan/manhattan.ts'\nimport type { GRIN2ViewData } from '../GRIN2Types'\n\n// Styling constants used only by the results view\nconst sectionMargin = '20px 0'\nconst btnMargin = '10px'\nconst headerMargin = '0 10px 0 0'\nconst headerFontSize = 14\nconst statsTableFontWeight = 'bold'\nconst backgroundColor = '#f8f8f8'\n\n/** Renders Manhattan plot + top genes table + run stats from precomputed ViewData. */\nexport class GRIN2ResultsView {\n\tprivate holder: any\n\tprivate app: any\n\n\tconstructor(holder: any, app: any) {\n\t\tthis.holder = holder\n\t\tthis.app = app\n\t}\n\n\tclear() {\n\t\tthis.holder.selectAll('*').remove()\n\t}\n\n\trender(viewData: GRIN2ViewData) {\n\t\tif (viewData.manhattan) {\n\t\t\tplotManhattan(this.holder, viewData.manhattan.plotData, viewData.manhattan.settings, this.app)\n\t\t}\n\n\t\tif (viewData.topGenes) {\n\t\t\tconst { headerText, columns, rows, dataItems } = viewData.topGenes\n\t\t\tconst tableContainer = this.holder.append('div').style('margin', sectionMargin)\n\n\t\t\tconst headerDiv = tableContainer\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('align-items', 'center')\n\t\t\t\t.style('margin', btnMargin)\n\n\t\t\theaderDiv.append('h3').style('margin', headerMargin).style('font-size', `${headerFontSize}px`).text(headerText)\n\n\t\t\tshowResultsTable({\n\t\t\t\ttableDiv: tableContainer.append('div'),\n\t\t\t\tapp: this.app,\n\t\t\t\tcolumns,\n\t\t\t\trows,\n\t\t\t\tdataItems,\n\t\t\t\tgetRowKey: (row: any) => row[0]?.value,\n\t\t\t\tmatrixButtonFormat: 'Matrix ({n} genes selected)',\n\t\t\t\tmaxHeight: '400px',\n\t\t\t\tmaxWidth: '100%',\n\t\t\t\tdataTestId: 'sjpp-grin2-top-genes-table',\n\t\t\t\tresize: 'both',\n\t\t\t\tselectAll: false,\n\t\t\t\tallowRestoreRowOrder: true,\n\t\t\t\trestoreButtonInFooter: true,\n\t\t\t\tdownload: {\n\t\t\t\t\tfileName: `grin2_top_genes_${new Date().toISOString().replace(/[:.]/g, '-').slice(0, -5)}.tsv`\n\t\t\t\t},\n\t\t\t\theader: {\n\t\t\t\t\tallowSort: true,\n\t\t\t\t\tstyle: {\n\t\t\t\t\t\t'font-weight': statsTableFontWeight,\n\t\t\t\t\t\t'background-color': backgroundColor\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\tif (viewData.statsSections.length > 0) {\n\t\t\tconst tablesContainer = this.holder.append('div').style('margin-top', '50px')\n\t\t\tfor (const section of viewData.statsSections) {\n\t\t\t\ttablesContainer\n\t\t\t\t\t.append('h4')\n\t\t\t\t\t.style('margin', headerMargin)\n\t\t\t\t\t.style('margin-top', '15px')\n\t\t\t\t\t.style('font-size', `${headerFontSize - 2}px`)\n\t\t\t\t\t.text(section.name)\n\n\t\t\t\tconst table = table2col({ holder: tablesContainer.append('div'), margin: '2px 8px' })\n\t\t\t\tfor (const [k, v] of section.rows) {\n\t\t\t\t\ttable.addRow(k, v)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n", "import { dt2lesion } from '#shared/common.js'\n\n/** CNV form fallbacks used when the dataset config does not supply ds-specific cutoffs. */\nexport const CNV_LOSS_THRESHOLD_FALLBACK = -0.4\nexport const CNV_GAIN_THRESHOLD_FALLBACK = 0.4\nexport const CNV_MAX_SEG_LENGTH_FALLBACK = 2_000_000\n\n/** Hypermutator cutoffs: a sample with more than this many raw records for a data type is excluded from\n * that data type (0 disables). SNV/indel counts mutation burden (source-agnostic), so 8000 is a safe\n * default. CNV counts *segments*, which varies hugely by data source: sparse for GDC's categorical cnv\n * (~30/case) but hundreds-to-thousands for dense native segmentation \u2014 where a fixed 500 silently drops\n * whole-sample CNV (esp. aneuploid, gain-heavy samples). So CNV defaults OFF (opt-in); set it per-run when\n * the source warrants it. */\nexport const SNVINDEL_HYPERMUTATOR_FALLBACK = 8000\nexport const CNV_HYPERMUTATOR_FALLBACK = 0\n\n/** How a dataset quantifies cnv values; declared at ds.queries.cnv.type. Mirrors CnvSegmentQuery in #types. */\nexport type CnvType = 'log2ratio' | 'segmean' | 'category' | 'copyNumber'\n\n/** Per-type defaults and slider bounds for the GRIN2 CNV threshold controls.\n * - log2ratio/segmean: diploid baseline 0 (loss<0, gain>0)\n * - copyNumber: absolute integer copy number, diploid baseline 2 (loss<=1, gain>=3, neutral=2)\n * - category: qualitative gain/loss call, no numeric thresholds (controls hidden) */\nexport type CnvTypeConfig = {\n\tlossDefault: number\n\tgainDefault: number\n\tlossMin: number\n\tlossMax: number\n\tgainMin: number\n\tgainMax: number\n\tstep: number\n\t/** when true, the gain/loss threshold rows are not shown (qualitative call) */\n\thideThresholds: boolean\n\t/** appended to the threshold row labels to convey units */\n\tunitLabel: string\n}\n\nexport const CNV_TYPE_CONFIG: Record<CnvType, CnvTypeConfig> = {\n\tlog2ratio: {\n\t\tlossDefault: CNV_LOSS_THRESHOLD_FALLBACK,\n\t\tgainDefault: CNV_GAIN_THRESHOLD_FALLBACK,\n\t\tlossMin: -5,\n\t\tlossMax: 0,\n\t\tgainMin: 0,\n\t\tgainMax: 5,\n\t\tstep: 0.05,\n\t\thideThresholds: false,\n\t\tunitLabel: 'log2 ratio'\n\t},\n\tsegmean: {\n\t\tlossDefault: CNV_LOSS_THRESHOLD_FALLBACK,\n\t\tgainDefault: CNV_GAIN_THRESHOLD_FALLBACK,\n\t\tlossMin: -5,\n\t\tlossMax: 0,\n\t\tgainMin: 0,\n\t\tgainMax: 5,\n\t\tstep: 0.05,\n\t\thideThresholds: false,\n\t\tunitLabel: 'segment mean'\n\t},\n\tcopyNumber: {\n\t\tlossDefault: 1,\n\t\tgainDefault: 3,\n\t\tlossMin: 0,\n\t\tlossMax: 2,\n\t\tgainMin: 2,\n\t\tgainMax: 20,\n\t\tstep: 1,\n\t\thideThresholds: false,\n\t\tunitLabel: 'copy number'\n\t},\n\tcategory: {\n\t\tlossDefault: 0,\n\t\tgainDefault: 0,\n\t\tlossMin: 0,\n\t\tlossMax: 0,\n\t\tgainMin: 0,\n\t\tgainMax: 0,\n\t\tstep: 1,\n\t\thideThresholds: true,\n\t\tunitLabel: ''\n\t}\n}\n\n/** Default gene-overlap-fraction for the artifact-region mask: a gene is excluded when at least\n * this fraction of its span lies inside a selected blacklist region. The set of blacklist sources\n * (and whether the mask runs at all) comes from the per-source checkboxes, which are populated from\n * the genome's declared blacklists. */\nexport const EXCLUDE_OVERLAP_FRAC_FALLBACK = 0.5\n\nexport function getDefaultGRIN2Settings(opts: any) {\n\tconst defaults = {\n\t\tmanhattan: {\n\t\t\t// Core plot dimensions\n\t\t\tplotWidth: 1000,\n\t\t\tplotHeight: 400,\n\t\t\tpngDotRadius: 2,\n\n\t\t\t// Layout spacing\n\t\t\tyAxisX: 70,\n\t\t\tyAxisY: 40,\n\t\t\tyAxisSpace: 20,\n\t\t\txAxisLabelPad: 30,\n\t\t\tyAxisPad: 5,\n\t\t\taxisColor: '#545454',\n\t\t\tshowYAxisLine: true,\n\n\t\t\t// Typography\n\t\t\tfontSize: 12,\n\n\t\t\t// Legend settings\n\t\t\tshowLegend: true,\n\t\t\tlegendItemWidth: 80,\n\t\t\tlegendDotRadius: 3,\n\t\t\tlegendRightOffset: 15,\n\t\t\tlegendTextOffset: 12,\n\t\t\tlegendVerticalOffset: 4,\n\t\t\tlegendFontSize: 12,\n\n\t\t\t// Interactive dots\n\t\t\tshowInteractiveDots: true,\n\t\t\tinteractiveDotRadius: 2,\n\t\t\tinteractiveDotStrokeWidth: 1,\n\n\t\t\t// Download options\n\t\t\tshowDownload: true,\n\n\t\t\t// Max genes to show in table, interactive dots cap, and tooltip genes\n\t\t\tmaxGenesToShow: 500,\n\t\t\tinteractiveDotsCap: 5000,\n\t\t\tmaxTooltipGenes: 5,\n\n\t\t\t// Q-value threshold for significance indicators in the table, tooltips, and for determining which dots become interactive\n\t\t\tqValueThreshold: 0.05,\n\n\t\t\t// Colors for lesion types, derived from the shared dt2lesion source of truth so every data\n\t\t\t// type (incl. itd and any future dt) is covered without a parallel hardcoded list. Used for\n\t\t\t// table significance indicators and passed to the Manhattan renderer as dot colors.\n\t\t\tlesionTypeColors: Object.fromEntries(\n\t\t\t\tObject.values(dt2lesion).flatMap((d: any) => d.lesionTypes.map((lt: any) => [lt.lesionType, lt.color]))\n\t\t\t),\n\n\t\t\t// Threshold for the rust code when determining if we need to raise the cap value from the default\n\t\t\tmaxCappedPoints: 5,\n\n\t\t\t// Bin size for cap calculations\n\t\t\tbinSize: 10,\n\n\t\t\t// Hard cap regardless of data distribution\n\t\t\thardCap: 200\n\t\t}\n\t}\n\n\treturn Object.assign(defaults, opts?.overrides)\n}\n", "import { table2col, make_one_checkbox, make_radios } from '#dom'\nimport {\n\tdtsnvindel,\n\tmclass,\n\tdtcnv,\n\tdtfusionrna,\n\tdtsv,\n\tdtitd,\n\tproteinChangingMutations,\n\tdt2lesion,\n\tmclasscnvgain,\n\tmclasscnvAmp,\n\tmclasscnvloss,\n\tmclasscnvHomozygousDel,\n\tmclasscnvloh\n} from '#shared/common.js'\n\n// display order for categorical cnv-class checkboxes: gains first (gain, amplification), then losses\n// (heterozygous deletion, homozygous deletion) so the two deletions sit next to each other. Any class not\n// listed here (dataset-specific) is appended after, in its declared order.\nconst CNV_CLASS_ORDER = [mclasscnvgain, mclasscnvAmp, mclasscnvloss, mclasscnvHomozygousDel, mclasscnvloh]\nimport { filterInit } from '#filter'\nimport type { GRIN2ControlsCallbacks, DtUsage } from '../GRIN2Types'\nimport {\n\tCNV_MAX_SEG_LENGTH_FALLBACK,\n\tCNV_TYPE_CONFIG,\n\tEXCLUDE_OVERLAP_FRAC_FALLBACK,\n\tSNVINDEL_HYPERMUTATOR_FALLBACK,\n\tCNV_HYPERMUTATOR_FALLBACK\n} from '../settings/defaults'\nimport type { CnvType } from '../settings/defaults'\n\n// Styling constants used only by the controls view\nconst optionsTextFontSize = 12\nconst tableFontSize = 11\nconst inputWidth = '80px'\nconst inputPadding = '2px 4px'\nconst inputBorderColor = '#ddd'\nconst inputBorderRadius = '2px'\nconst checkboxContainerMaxHeight = '150px'\nconst checkboxContainerBorder = '1px solid #ddd'\nconst controlGap = '8px'\nconst checkboxMarginBottom = '2px'\n// shared width for the \"Consequences\" / \"Classes\" label cells so their checkbox boxes line up vertically\n// (each lives in its own table2col, whose label column would otherwise size to its own label text)\nconst checkboxRowLabelWidth = '110px'\n\n/** Builds and owns the GRIN2 config form (citation header + data-type rows + run button).\n *  Reads its own state from the live DOM and exposes it to the controller via getDtUsage/getConfigValues. */\nexport class GRIN2ControlsView {\n\tprivate headerHolder: any\n\tprivate controlsHolder: any\n\tprivate actionsHolder: any\n\tprivate config: any\n\tprivate vocabApi: any\n\tprivate callbacks: GRIN2ControlsCallbacks\n\n\tprivate snvindelCheckbox: any = null\n\tprivate cnvCheckbox: any = null\n\tprivate fusionCheckbox: any = null\n\tprivate svCheckbox: any = null\n\tprivate itdCheckbox: any = null\n\tprivate runButton: any = null\n\tprivate consequenceCheckboxes: Record<string, any> = {}\n\tprivate snvindelSelectAllBtn: any = null\n\tprivate snvindelClearAllBtn: any = null\n\tprivate snvindelDefaultBtn: any = null\n\t// one checkbox per supported categorical cnv-segment class (populated only for ds.queries.cnv.type='category')\n\tprivate cnvCategoryCheckboxes: Record<string, any> = {}\n\n\tprivate cnv_lossThreshold: any = null\n\tprivate cnv_gainThreshold: any = null\n\tprivate cnv_maxSegLength: any = null\n\tprivate cnv_hyperMutator: any = null\n\tprivate snvindel_hyperMutator: any = null\n\t/** how this ds quantifies cnv values; from the selected cnv type or ds.queries.cnv.type, default 'log2ratio' */\n\tprivate cnvType: CnvType = 'log2ratio'\n\t/** id of the user-selected cnv file type, when the ds exposes singleSampleMutation.cnvTypes (else null) */\n\tprivate cnvSelectedTypeId: string | null = null\n\n\t// one checkbox per genome-declared blacklist source, keyed by source name\n\tprivate excludeCheckboxes: Record<string, any> = {}\n\tprivate exclude_overlapFrac: any = null\n\n\tprivate snvindelMafFilter: any = null\n\n\tprivate genome: any\n\n\tconstructor(opts: {\n\t\theaderHolder: any\n\t\tcontrolsHolder: any\n\t\tconfig: any\n\t\tvocabApi: any\n\t\tgenome: any\n\t\tactionsHolder: any\n\t\tcallbacks: GRIN2ControlsCallbacks\n\t}) {\n\t\tthis.headerHolder = opts.headerHolder\n\t\tthis.controlsHolder = opts.controlsHolder\n\t\tthis.config = opts.config\n\t\tthis.vocabApi = opts.vocabApi\n\t\tthis.genome = opts.genome\n\t\tthis.actionsHolder = opts.actionsHolder\n\t\tthis.callbacks = opts.callbacks\n\t}\n\n\tbuild() {\n\t\tthis.headerHolder\n\t\t\t.style('margin', '15px')\n\t\t\t.html(\n\t\t\t\t'GRIN2 stands for Genomic Random Interval (GRIN) statistical model. For details, see <a href=https://pubmed.ncbi.nlm.nih.gov/23842812/ target=_blank>Pounds, S. et al. Bioinformatics 2013</a>.'\n\t\t\t)\n\n\t\tconst table = table2col({ holder: this.controlsHolder, disableScroll: true })\n\t\tconst queries = this.vocabApi.termdbConfig.queries\n\t\tif (queries.snvindel) this.addSnvindelRow(table)\n\t\tif (queries.cnv || queries.singleSampleMutation?.cnvTypes?.length) this.addCnvRow(table)\n\t\tif (queries.svfusion?.dtLst?.includes(dtfusionrna)) this.addFusionRow(table)\n\t\tif (queries.svfusion?.dtLst?.includes(dtsv)) this.addSvRow(table)\n\t\tif (queries.itd) this.addItdRow(table)\n\n\t\t// Artifact-region exclude mask (applies to all lesion types).\n\t\tthis.addExcludeRow(table)\n\n\t\tthis.runButton = this.actionsHolder\n\t\t\t.append('button')\n\t\t\t.attr('data-testid', 'sjpp-grin2-run-button')\n\t\t\t.text('Run GRIN2')\n\t\t\t.on('click', () => this.callbacks.onRun())\n\n\t\tthis.updateRunButtonFromCheckboxes()\n\t}\n\n\tgetDtUsage(): DtUsage {\n\t\tconst dtUsage = structuredClone(this.config.settings.dtUsage) as DtUsage\n\t\tif (dtUsage[dtsnvindel]) dtUsage[dtsnvindel].checked = this.snvindelCheckbox.property('checked')\n\t\tif (dtUsage[dtcnv]) dtUsage[dtcnv].checked = this.cnvCheckbox.property('checked')\n\t\tif (dtUsage[dtfusionrna]) dtUsage[dtfusionrna].checked = this.fusionCheckbox.property('checked')\n\t\tif (dtUsage[dtsv]) dtUsage[dtsv].checked = this.svCheckbox.property('checked')\n\t\tif (dtUsage[dtitd]) dtUsage[dtitd].checked = this.itdCheckbox.property('checked')\n\t\treturn dtUsage\n\t}\n\n\tgetConfigValues(dtUsage: DtUsage): any {\n\t\tconst requestConfig: any = {}\n\t\tif (dtUsage[dtsnvindel]?.checked) {\n\t\t\trequestConfig.snvindelOptions = {\n\t\t\t\tconsequences: this.getSelectedConsequences()\n\t\t\t}\n\t\t\tif (this.snvindel_hyperMutator) {\n\t\t\t\t// a cleared input yields NaN; fall back to the default so we never send NaN (which would silently\n\t\t\t\t// disable the cutoff server-side and leak \"NaN\" into summary strings)\n\t\t\t\tconst v = parseFloat(this.snvindel_hyperMutator.property('value'))\n\t\t\t\trequestConfig.snvindelOptions.hyperMutator = Number.isFinite(v) ? v : SNVINDEL_HYPERMUTATOR_FALLBACK\n\t\t\t}\n\t\t\tif (this.snvindelMafFilter) {\n\t\t\t\trequestConfig.snvindelOptions.mafFilter = this.snvindelMafFilter\n\t\t\t}\n\t\t}\n\t\tif (dtUsage[dtcnv]?.checked) {\n\t\t\trequestConfig.cnvOptions = {\n\t\t\t\tmaxSegLength: parseFloat(this.cnv_maxSegLength.property('value'))\n\t\t\t}\n\t\t\tif (this.cnv_hyperMutator) {\n\t\t\t\t// cleared input => NaN; fall back to the default (see snvindel hyperMutator above)\n\t\t\t\tconst v = parseFloat(this.cnv_hyperMutator.property('value'))\n\t\t\t\trequestConfig.cnvOptions.hyperMutator = Number.isFinite(v) ? v : CNV_HYPERMUTATOR_FALLBACK\n\t\t\t}\n\t\t\t// id of the selected cnv file type (datasets exposing singleSampleMutation.cnvTypes, e.g. GDC)\n\t\t\tif (this.cnvSelectedTypeId) requestConfig.cnvOptions.cnvType = this.cnvSelectedTypeId\n\t\t\t// 'category' is a qualitative call with no numeric thresholds; the rows aren't rendered\n\t\t\tif (this.cnv_lossThreshold && this.cnv_gainThreshold) {\n\t\t\t\trequestConfig.cnvOptions.lossThreshold = parseFloat(this.cnv_lossThreshold.property('value'))\n\t\t\t\trequestConfig.cnvOptions.gainThreshold = parseFloat(this.cnv_gainThreshold.property('value'))\n\t\t\t}\n\t\t\t// categorical cnv: the checked cnv-segment classes to include (e.g. GDC gain/loss/amp/homdel)\n\t\t\tif (Object.keys(this.cnvCategoryCheckboxes).length) {\n\t\t\t\trequestConfig.cnvOptions.cnvCategories = this.getSelectedCnvCategories()\n\t\t\t}\n\t\t}\n\t\tif (dtUsage[dtfusionrna]?.checked) requestConfig.fusionOptions = {}\n\t\tif (dtUsage[dtsv]?.checked) requestConfig.svOptions = {}\n\t\tif (dtUsage[dtitd]?.checked) requestConfig.itdOptions = {}\n\t\t// excludeOptions.blacklists = names of the checked genome-declared sources.\n\t\t// Only emitted when the genome declares blacklists (otherwise the mask is unavailable).\n\t\tif (Object.keys(this.excludeCheckboxes).length > 0) {\n\t\t\tconst blacklists = Object.entries(this.excludeCheckboxes)\n\t\t\t\t.filter(([, cb]) => cb.property('checked'))\n\t\t\t\t.map(([name]) => name)\n\t\t\tconst overlapFracRaw = this.exclude_overlapFrac\n\t\t\t\t? parseFloat(this.exclude_overlapFrac.property('value'))\n\t\t\t\t: EXCLUDE_OVERLAP_FRAC_FALLBACK\n\t\t\trequestConfig.excludeOptions = {\n\t\t\t\tblacklists,\n\t\t\t\toverlapFrac: Number.isFinite(overlapFracRaw) ? overlapFracRaw : EXCLUDE_OVERLAP_FRAC_FALLBACK\n\t\t\t}\n\t\t}\n\t\treturn requestConfig\n\t}\n\n\tsetBusy(busy: boolean) {\n\t\tthis.controlsHolder?.style('pointer-events', busy ? 'none' : 'auto').style('opacity', busy ? '0.5' : '1')\n\t\tthis.runButton?.property('disabled', busy).text(busy ? 'Running GRIN2...' : 'Run GRIN2')\n\t}\n\n\tprivate updateRunButtonFromCheckboxes() {\n\t\tconst dtUsage = this.snvindelCheckbox ? this.getDtUsage() : (this.config.settings.dtUsage as DtUsage)\n\t\t// A run needs at least one data type that would actually contribute data. A ticked data type usually\n\t\t// qualifies, except when it has an explicit include-list with nothing selected: snvindel with no\n\t\t// consequence checked, or categorical CNV with no class checked, both match nothing (an empty list =\n\t\t// \"include none\"), so they can't drive a run on their own.\n\t\tconst anyEffective = Object.entries(dtUsage).some(([dt, info]) => {\n\t\t\tif (!info.checked) return false\n\t\t\tif (Number(dt) === dtsnvindel && Object.keys(this.consequenceCheckboxes).length > 0) {\n\t\t\t\treturn this.getSelectedConsequences().length > 0\n\t\t\t}\n\t\t\tif (Number(dt) === dtcnv && Object.keys(this.cnvCategoryCheckboxes).length > 0) {\n\t\t\t\treturn this.getSelectedCnvCategories().length > 0\n\t\t\t}\n\t\t\treturn true\n\t\t})\n\t\tthis.runButton?.property('disabled', !anyEffective)\n\t}\n\n\tprivate getSelectedConsequences(): string[] {\n\t\tconst consequences: string[] = []\n\t\tObject.entries(this.consequenceCheckboxes).forEach(([classKey, checkbox]) => {\n\t\t\tif (checkbox.property('checked')) consequences.push(classKey)\n\t\t})\n\t\treturn consequences\n\t}\n\n\tprivate addSnvindelRow(table: any) {\n\t\tconst [left, right] = table.addRow()\n\t\tconst t2 = table2col({ holder: right })\n\n\t\t// Consequences section header + checkbox grid\n\t\t{\n\t\t\tconst [labelCell, containerCell] = t2.addRow()\n\t\t\tlabelCell.text('Consequences').style('padding-top', '8px').style('min-width', checkboxRowLabelWidth)\n\t\t\tthis.createConsequenceCheckboxes(containerCell)\n\t\t}\n\n\t\t// MAF filter UI (only if dataset config provides it)\n\t\tconst mafFilterConfig = this.vocabApi.termdbConfig.queries?.snvindel?.mafFilter\n\t\tif (mafFilterConfig) {\n\t\t\tthis.snvindelMafFilter = structuredClone(\n\t\t\t\tthis.config.settings?.snvindelOptions?.mafFilter || mafFilterConfig.filter\n\t\t\t)\n\t\t\tconst [td1, td2] = t2.addRow()\n\t\t\ttd1.text('MAF filter')\n\t\t\tfilterInit({\n\t\t\t\temptyLabel: '+',\n\t\t\t\tholder: td2,\n\t\t\t\theader_mode: 'hide_search',\n\t\t\t\tvocab: { terms: mafFilterConfig.terms },\n\t\t\t\tcallback: async (filter: any) => {\n\t\t\t\t\tthis.snvindelMafFilter = filter\n\t\t\t\t}\n\t\t\t}).main(this.snvindelMafFilter)\n\t\t}\n\n\t\t// Hypermutator cutoff: samples with more SNV/indel records than this are excluded from snvindel (0 disables)\n\t\tthis.snvindel_hyperMutator = this.addOptionRowToTable(\n\t\t\tt2,\n\t\t\t'Hypermutator Cutoff',\n\t\t\tthis.config.settings?.snvindelOptions?.hyperMutator ?? SNVINDEL_HYPERMUTATOR_FALLBACK,\n\t\t\t0,\n\t\t\tundefined,\n\t\t\t1\n\t\t).attr('title', 'Exclude a sample from SNV/indel when it has more than this many records. 0 disables.')\n\n\t\tconst isChecked = this.config.settings.dtUsage[dtsnvindel].checked\n\t\tt2.table.style('display', isChecked ? '' : 'none')\n\t\tthis.snvindelCheckbox = make_one_checkbox({\n\t\t\tholder: left,\n\t\t\tlabeltext: dt2lesion[dtsnvindel].uilabel,\n\t\t\tchecked: isChecked,\n\t\t\ttestid: 'sjpp-grin2-checkbox-snvindel',\n\t\t\tcallback: (checked: boolean) => {\n\t\t\t\tt2.table.style('display', checked ? '' : 'none')\n\t\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t\t}\n\t\t})\n\t}\n\n\tprivate addCnvRow(table: any) {\n\t\tconst [left, right] = table.addRow()\n\t\t// container toggled by the cnv checkbox; holds the type radios (if any) + threshold inputs\n\t\tconst cnvBody = right.append('div')\n\n\t\t// Only use saved CNV settings if a previous run completed\n\t\tconst useSaved = this.config.settings.runAnalysis === true\n\t\tconst savedCnv = useSaved ? this.config.settings.cnvOptions : undefined\n\t\tconst cnvQuery = this.vocabApi.termdbConfig.queries.cnv\n\t\t// datasets that serve multiple cnv file types per sample (e.g. GDC masked vs allele-specific)\n\t\tconst cnvTypes = this.vocabApi.termdbConfig.queries.singleSampleMutation?.cnvTypes as\n\t\t\t| { id: string; label: string; valueType: CnvType; dataType: string }[]\n\t\t\t| undefined\n\n\t\t// radios (if any) sit above the threshold inputs, which are rebuilt when the selected type changes\n\t\tconst radioHolder = cnvTypes?.length ? cnvBody.append('div').style('margin-bottom', '6px') : null\n\t\tconst thresholdHolder = cnvBody.append('div')\n\n\t\tif (cnvTypes?.length) {\n\t\t\t// initial selection: a saved & still-valid type, else the first declared type\n\t\t\tconst savedId = savedCnv?.cnvType\n\t\t\tthis.cnvSelectedTypeId = (savedId && cnvTypes.find(t => t.id === savedId)?.id) || cnvTypes[0].id\n\n\t\t\t// one radio per declared cnv type; switching rebuilds the threshold rows for the new valueType\n\t\t\tmake_radios({\n\t\t\t\tholder: radioHolder,\n\t\t\t\toptions: cnvTypes.map(t => ({\n\t\t\t\t\tlabel: t.label,\n\t\t\t\t\tvalue: t.id,\n\t\t\t\t\tchecked: t.id === this.cnvSelectedTypeId,\n\t\t\t\t\ttestid: `sjpp-grin2-cnvtype-${t.id}`\n\t\t\t\t})),\n\t\t\t\tstyles: { display: 'block' },\n\t\t\t\tcallback: (value: string) => {\n\t\t\t\t\tthis.cnvSelectedTypeId = value\n\t\t\t\t\tconst def = cnvTypes.find(t => t.id === value)\n\t\t\t\t\t// only reuse saved thresholds when the user is back on the saved type; otherwise show defaults\n\t\t\t\t\tconst savedForType = value === savedCnv?.cnvType ? savedCnv : undefined\n\t\t\t\t\tthis.renderCnvThresholdRows(thresholdHolder, def?.valueType ?? 'log2ratio', savedForType, cnvQuery)\n\t\t\t\t}\n\t\t\t})\n\t\t} else {\n\t\t\tthis.cnvSelectedTypeId = null\n\t\t}\n\n\t\t// initial threshold rows. valueType from the selected type (cnvTypes ds) or ds-level cnv.type (file ds)\n\t\tconst initialValueType: CnvType =\n\t\t\t(cnvTypes?.length ? cnvTypes.find(t => t.id === this.cnvSelectedTypeId)?.valueType : cnvQuery?.type) ??\n\t\t\t'log2ratio'\n\t\t// savedCnv only applies to the initially-selected type (or to the single-type file ds case)\n\t\tconst initialSaved = !cnvTypes?.length || this.cnvSelectedTypeId === savedCnv?.cnvType ? savedCnv : undefined\n\t\tthis.renderCnvThresholdRows(thresholdHolder, initialValueType, initialSaved, cnvQuery)\n\n\t\tconst dtUsage = this.config.settings.dtUsage\n\t\tconst isChecked =\n\t\t\tuseSaved && dtUsage[dtcnv]?.checked !== undefined ? dtUsage[dtcnv].checked : !!(cnvQuery || cnvTypes?.length)\n\t\tcnvBody.style('display', isChecked ? '' : 'none')\n\n\t\tthis.cnvCheckbox = make_one_checkbox({\n\t\t\tholder: left,\n\t\t\tlabeltext: dt2lesion[dtcnv].uilabel,\n\t\t\tchecked: isChecked,\n\t\t\ttestid: 'sjpp-grin2-checkbox-cnv',\n\t\t\tcallback: (checked: boolean) => {\n\t\t\t\tcnvBody.style('display', checked ? '' : 'none')\n\t\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t\t}\n\t\t})\n\t}\n\n\t/** (Re)build the loss/gain/maxSeg inputs for a given cnv value type. Called on first render and whenever\n\t *  the user switches cnv type \u2014 segmean/copyNumber/log2ratio have type-specific defaults and ranges, and\n\t *  'category' is qualitative and hides the thresholds entirely. */\n\tprivate renderCnvThresholdRows(holder: any, valueType: CnvType, savedCnv: any, cnvQuery: any) {\n\t\tholder.selectAll('*').remove()\n\t\tthis.cnvType = valueType\n\t\tconst cfg = CNV_TYPE_CONFIG[valueType]\n\t\t// reset per-render; only categorical cnv populates category checkboxes (below)\n\t\tthis.cnvCategoryCheckboxes = {}\n\n\t\tif (cfg.hideThresholds) {\n\t\t\t// qualitative call: no numeric thresholds; instead offer one checkbox per supported cnv-segment\n\t\t\t// class (mirrors the snvindel consequence checkboxes). Rendered in its own table (before the\n\t\t\t// Max Segment Length table below) so that label doesn't widen the \"Classes\" column, keeping the\n\t\t\t// checkbox box aligned with \"Consequences\" above. Clear stale threshold inputs.\n\t\t\tthis.cnv_lossThreshold = null\n\t\t\tthis.cnv_gainThreshold = null\n\t\t\tthis.createCnvCategoryCheckboxes(holder, savedCnv)\n\t\t}\n\n\t\tconst t2 = table2col({ holder })\n\n\t\tif (!cfg.hideThresholds) {\n\t\t\tthis.cnv_lossThreshold = this.addOptionRowToTable(\n\t\t\t\tt2,\n\t\t\t\tcfg.unitLabel ? `Loss Threshold (${cfg.unitLabel})` : 'Loss Threshold',\n\t\t\t\tsavedCnv?.lossThreshold ?? cnvQuery?.cnvLossCutoff ?? cfg.lossDefault,\n\t\t\t\tcfg.lossMin,\n\t\t\t\tcfg.lossMax,\n\t\t\t\tcfg.step\n\t\t\t)\n\t\t\tthis.cnv_gainThreshold = this.addOptionRowToTable(\n\t\t\t\tt2,\n\t\t\t\tcfg.unitLabel ? `Gain Threshold (${cfg.unitLabel})` : 'Gain Threshold',\n\t\t\t\tsavedCnv?.gainThreshold ?? cnvQuery?.cnvGainCutoff ?? cfg.gainDefault,\n\t\t\t\tcfg.gainMin,\n\t\t\t\tcfg.gainMax,\n\t\t\t\tcfg.step\n\t\t\t)\n\t\t}\n\t\tthis.cnv_maxSegLength = this.addOptionRowToTable(\n\t\t\tt2,\n\t\t\t'Max Segment Length',\n\t\t\tsavedCnv?.maxSegLength ?? cnvQuery?.cnvMaxLength ?? CNV_MAX_SEG_LENGTH_FALLBACK,\n\t\t\t0,\n\t\t\t1e9,\n\t\t\t1000\n\t\t)\n\t\t// Hypermutator cutoff: samples with more cnv segments than this are excluded from cnv (0 disables)\n\t\tthis.cnv_hyperMutator = this.addOptionRowToTable(\n\t\t\tt2,\n\t\t\t'Hypermutator Cutoff',\n\t\t\tsavedCnv?.hyperMutator ?? CNV_HYPERMUTATOR_FALLBACK,\n\t\t\t0,\n\t\t\tundefined,\n\t\t\t1\n\t\t).attr('title', 'Exclude a sample from CNV when it has more than this many segments. 0 disables.')\n\t}\n\n\tprivate addFusionRow(table: any) {\n\t\tconst [left, right] = table.addRow()\n\t\tconst t2 = table2col({ holder: right })\n\t\tconst isChecked = this.config.settings.dtUsage[dtfusionrna].checked\n\t\tt2.table.style('display', isChecked ? '' : 'none')\n\n\t\tthis.fusionCheckbox = make_one_checkbox({\n\t\t\tholder: left,\n\t\t\tlabeltext: dt2lesion[dtfusionrna].uilabel,\n\t\t\tchecked: isChecked,\n\t\t\ttestid: 'grin2-checkbox-fusion',\n\t\t\tcallback: (checked: boolean) => {\n\t\t\t\tt2.table.style('display', checked ? '' : 'none')\n\t\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t\t}\n\t\t})\n\t}\n\n\tprivate addSvRow(table: any) {\n\t\tconst [left, right] = table.addRow()\n\t\tconst t2 = table2col({ holder: right })\n\t\tconst isChecked = this.config.settings.dtUsage[dtsv].checked\n\t\tt2.table.style('display', isChecked ? '' : 'none')\n\n\t\tthis.svCheckbox = make_one_checkbox({\n\t\t\tholder: left,\n\t\t\tlabeltext: dt2lesion[dtsv].uilabel,\n\t\t\tchecked: isChecked,\n\t\t\ttestid: 'sjpp-grin2-checkbox-sv',\n\t\t\tcallback: (checked: boolean) => {\n\t\t\t\tt2.table.style('display', checked ? '' : 'none')\n\t\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t\t}\n\t\t})\n\t}\n\n\tprivate addItdRow(table: any) {\n\t\tconst [left, right] = table.addRow()\n\t\tconst t2 = table2col({ holder: right })\n\t\tconst isChecked = this.config.settings.dtUsage[dtitd].checked\n\t\tt2.table.style('display', isChecked ? '' : 'none')\n\n\t\tthis.itdCheckbox = make_one_checkbox({\n\t\t\tholder: left,\n\t\t\tlabeltext: dt2lesion[dtitd].uilabel,\n\t\t\tchecked: isChecked,\n\t\t\ttestid: 'sjpp-grin2-checkbox-itd',\n\t\t\tcallback: (checked: boolean) => {\n\t\t\t\tt2.table.style('display', checked ? '' : 'none')\n\t\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t\t}\n\t\t})\n\t}\n\n\t/** Artifact-region mask row. Renders one checkbox per blacklist source declared for the genome\n\t * (Genome.blacklists, exposed to the client as {name}[]), plus the gene-overlap-fraction input.\n\t * Skipped entirely when the genome declares no blacklists. Unchecking all sources disables the\n\t * mask (server resolves an empty source list to no masking). */\n\tprivate addExcludeRow(table: any) {\n\t\tconst blacklists: { name: string }[] = this.genome?.blacklists || []\n\t\tif (!blacklists.length) return\n\n\t\tconst [left, right] = table.addRow()\n\t\tleft.text('Exclude genes overlapping').style('padding-top', '4px')\n\n\t\t// default = all sources on; if a previous run saved a selection, restore exactly that set\n\t\tconst savedExclude = this.config.settings.runAnalysis === true ? this.config.settings.excludeOptions : undefined\n\t\tconst savedNames: string[] | undefined = savedExclude?.blacklists\n\t\tconst isChecked = (name: string) => (savedNames ? savedNames.includes(name) : true)\n\n\t\tthis.excludeCheckboxes = {}\n\t\tconst cbContainer = right.append('div').style('margin-bottom', '6px')\n\t\tblacklists.forEach(bl => {\n\t\t\tconst div = cbContainer.append('div').style('margin-bottom', checkboxMarginBottom)\n\t\t\tthis.excludeCheckboxes[bl.name] = make_one_checkbox({\n\t\t\t\tholder: div,\n\t\t\t\tlabeltext: bl.name,\n\t\t\t\tchecked: isChecked(bl.name),\n\t\t\t\tdivstyle: { 'font-size': `${tableFontSize}px` },\n\t\t\t\tcallback: () => {}\n\t\t\t})\n\t\t})\n\n\t\tconst t2 = table2col({ holder: right })\n\t\tthis.exclude_overlapFrac = this.addOptionRowToTable(\n\t\t\tt2,\n\t\t\t'Min gene overlap',\n\t\t\tsavedExclude?.overlapFrac ?? EXCLUDE_OVERLAP_FRAC_FALLBACK,\n\t\t\t0,\n\t\t\t1,\n\t\t\t0.05\n\t\t)\n\t}\n\n\tprivate addOptionRowToTable(\n\t\ttable: any,\n\t\tlabel: string,\n\t\tdefaultValue: number,\n\t\tmin?: number,\n\t\tmax?: number,\n\t\tstep?: number\n\t) {\n\t\tconst [labelCell, inputCell] = table.addRow()\n\t\tlabelCell.text(label)\n\n\t\tconst input = inputCell\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr('value', defaultValue)\n\t\t\t.style('width', inputWidth)\n\t\t\t.style('padding', inputPadding)\n\t\t\t.style('border', `1px solid ${inputBorderColor}`)\n\t\t\t.style('border-radius', inputBorderRadius)\n\t\t\t.style('font-size', `${optionsTextFontSize}px`)\n\n\t\tif (min !== null && min !== undefined) input.attr('min', min)\n\t\tif (max !== null && max !== undefined) input.attr('max', max)\n\t\tif (step !== null && step !== undefined) input.attr('step', step)\n\t\treturn input\n\t}\n\n\tprivate createConsequenceCheckboxes(container: any) {\n\t\tconst snvIndelClasses = Object.entries(mclass).filter(\n\t\t\t([key, cls]: [string, any]) => cls.dt === dtsnvindel && key !== 'Blank' && key !== 'WT'\n\t\t)\n\n\t\tconst saved = this.config.settings.snvindelOptions?.consequences as string[] | undefined\n\t\tconst useSaved = this.config.settings.runAnalysis === true && !!saved && saved.length > 0\n\t\tconst canonicalDefault = new Set<string>([...proteinChangingMutations, 'StartLost', 'StopLost'])\n\t\tconst initialChecked = useSaved ? new Set<string>(saved!) : canonicalDefault\n\n\t\tconst controlDiv = container\n\t\t\t.append('div')\n\t\t\t.style('margin-bottom', '6px')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('gap', controlGap)\n\n\t\tthis.snvindelSelectAllBtn = controlDiv.append('button').style('font-size', `${tableFontSize}px`).text('Select All')\n\t\tthis.snvindelClearAllBtn = controlDiv.append('button').style('font-size', `${tableFontSize}px`).text('Clear All')\n\t\tthis.snvindelDefaultBtn = controlDiv.append('button').style('font-size', `${tableFontSize}px`).text('Default')\n\n\t\tconst checkboxContainer = container\n\t\t\t.append('div')\n\t\t\t.style('max-height', checkboxContainerMaxHeight)\n\t\t\t.style('overflow-y', 'auto')\n\t\t\t.style('border', checkboxContainerBorder)\n\n\t\tthis.consequenceCheckboxes = {}\n\t\tsnvIndelClasses.forEach(([classKey, classInfo]: [string, any]) => {\n\t\t\tconst checkboxDiv = checkboxContainer.append('div').style('margin-bottom', checkboxMarginBottom)\n\t\t\tconst checkbox = make_one_checkbox({\n\t\t\t\tholder: checkboxDiv,\n\t\t\t\tlabeltext: classInfo.label,\n\t\t\t\tchecked: initialChecked.has(classKey),\n\t\t\t\tdivstyle: { 'font-size': `${tableFontSize}px` },\n\t\t\t\t// clearing every consequence includes nothing, which can disable the run button (see\n\t\t\t\t// updateRunButtonFromCheckboxes), so re-evaluate it on each toggle\n\t\t\t\tcallback: () => this.updateRunButtonFromCheckboxes()\n\t\t\t})\n\t\t\tcheckboxDiv.select('label').attr('title', classInfo.desc)\n\t\t\tthis.consequenceCheckboxes[classKey] = checkbox\n\t\t})\n\n\t\tthis.snvindelSelectAllBtn.on('click', () => {\n\t\t\tObject.values(this.consequenceCheckboxes).forEach(cb => cb.property('checked', true))\n\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t})\n\t\tthis.snvindelClearAllBtn.on('click', () => {\n\t\t\tObject.values(this.consequenceCheckboxes).forEach(cb => cb.property('checked', false))\n\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t})\n\t\tthis.snvindelDefaultBtn.on('click', () => {\n\t\t\tObject.entries(this.consequenceCheckboxes).forEach(([classKey, checkbox]) => {\n\t\t\t\tcheckbox.property('checked', canonicalDefault.has(classKey))\n\t\t\t})\n\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t})\n\t}\n\n\tprivate getSelectedCnvCategories(): string[] {\n\t\tconst categories: string[] = []\n\t\tObject.entries(this.cnvCategoryCheckboxes).forEach(([classKey, checkbox]) => {\n\t\t\tif (checkbox.property('checked')) categories.push(classKey)\n\t\t})\n\t\treturn categories\n\t}\n\n\t/** One checkbox per categorical cnv-segment class supported by this dataset, all checked by default \u2014\n\t * the cnv analog of the snvindel consequence checkboxes. The supported classes are the CNV entries the\n\t * dataset declares in termdbConfig.mclass (e.g. GDC: Gain / Heterozygous Deletion / Amplification /\n\t * Homozygous Deletion), identified via the global mclass dt; labels prefer the dataset override. Rendered\n\t * in its own table2col with a fixed label width so the checkbox box aligns with \"Consequences\" above. */\n\tprivate createCnvCategoryCheckboxes(holder: any, savedCnv: any) {\n\t\tconst dsMclass = this.vocabApi.termdbConfig?.mclass || {}\n\t\tconst cnvClasses = Object.keys(dsMclass)\n\t\t\t.filter(key => mclass[key]?.dt === dtcnv)\n\t\t\t.map(key => ({ key, label: dsMclass[key]?.label || mclass[key]?.label || key, desc: mclass[key]?.desc || '' }))\n\t\t\t// gains together, deletions together (see CNV_CLASS_ORDER); unlisted classes keep declared order at end\n\t\t\t.sort((a, b) => {\n\t\t\t\tconst ia = CNV_CLASS_ORDER.indexOf(a.key)\n\t\t\t\tconst ib = CNV_CLASS_ORDER.indexOf(b.key)\n\t\t\t\treturn (ia === -1 ? Infinity : ia) - (ib === -1 ? Infinity : ib)\n\t\t\t})\n\t\tthis.cnvCategoryCheckboxes = {}\n\t\tif (!cnvClasses.length) return\n\n\t\t// default = all classes on; restore an exact saved selection only after a completed run\n\t\tconst saved = savedCnv?.cnvCategories as string[] | undefined\n\t\tconst useSaved = this.config.settings.runAnalysis === true && Array.isArray(saved)\n\t\tconst initialChecked = useSaved ? new Set<string>(saved!) : new Set<string>(cnvClasses.map(c => c.key))\n\n\t\t// own table so the wide \"Max Segment Length\" label doesn't push these checkboxes right; fixed label\n\t\t// width matches the snvindel \"Consequences\" cell so the two checkbox boxes line up vertically\n\t\tconst t2 = table2col({ holder })\n\t\tconst [labelCell, containerCell] = t2.addRow()\n\t\tlabelCell.text('Classes').style('padding-top', '8px').style('min-width', checkboxRowLabelWidth)\n\n\t\tconst controlDiv = containerCell\n\t\t\t.append('div')\n\t\t\t.style('margin-bottom', '6px')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('gap', controlGap)\n\t\tconst selectAllBtn = controlDiv.append('button').style('font-size', `${tableFontSize}px`).text('Select All')\n\t\tconst clearAllBtn = controlDiv.append('button').style('font-size', `${tableFontSize}px`).text('Clear All')\n\n\t\tconst checkboxContainer = containerCell\n\t\t\t.append('div')\n\t\t\t.style('max-height', checkboxContainerMaxHeight)\n\t\t\t.style('overflow-y', 'auto')\n\t\t\t.style('border', checkboxContainerBorder)\n\t\t\t.style('margin-bottom', '6px')\n\n\t\tcnvClasses.forEach(c => {\n\t\t\tconst checkboxDiv = checkboxContainer.append('div').style('margin-bottom', checkboxMarginBottom)\n\t\t\tconst checkbox = make_one_checkbox({\n\t\t\t\tholder: checkboxDiv,\n\t\t\t\tlabeltext: c.label,\n\t\t\t\tchecked: initialChecked.has(c.key),\n\t\t\t\tdivstyle: { 'font-size': `${tableFontSize}px` },\n\t\t\t\t// clearing every class excludes all cnv, which can disable the run button (see\n\t\t\t\t// updateRunButtonFromCheckboxes), so re-evaluate it on each toggle\n\t\t\t\tcallback: () => this.updateRunButtonFromCheckboxes()\n\t\t\t})\n\t\t\tif (c.desc) checkboxDiv.select('label').attr('title', c.desc)\n\t\t\tthis.cnvCategoryCheckboxes[c.key] = checkbox\n\t\t})\n\n\t\tselectAllBtn.on('click', () => {\n\t\t\tObject.values(this.cnvCategoryCheckboxes).forEach(cb => cb.property('checked', true))\n\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t})\n\t\tclearAllBtn.on('click', () => {\n\t\t\tObject.values(this.cnvCategoryCheckboxes).forEach(cb => cb.property('checked', false))\n\t\t\tthis.updateRunButtonFromCheckboxes()\n\t\t})\n\t}\n}\n", "import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport type { BasePlotConfig, MassAppApi, MassState } from '#mass/types/mass'\nimport type { GRIN2Dom, GRIN2Opts } from './GRIN2Types'\nimport { GRIN2Model } from './model/GRIN2Model'\nimport { GRIN2ViewModel } from './viewModel/GRIN2ViewModel'\nimport { GRIN2ResultsView } from './view/GRIN2ResultsView'\nimport { GRIN2ControlsView } from './view/GRIN2ControlsView'\nimport { getDefaultGRIN2Settings } from './settings/defaults'\nimport { getCombinedTermFilter, getNormalRoot } from '#filter'\nimport { sayerror } from '#dom'\nimport { dtsnvindel, dtcnv, dtfusionrna, dtsv, dtitd, dt2lesion } from '#shared/common.js'\nimport { PlotBase } from '#plots/PlotBase.ts'\nimport { controlsInit } from '#plots/controls.js'\n\nclass GRIN2 extends PlotBase implements RxComponent {\n\tstatic type = 'grin2'\n\treadonly type = 'grin2'\n\tdom: GRIN2Dom\n\tcomponents: { controls: ComponentApi }\n\tprivate model!: GRIN2Model\n\tprivate resultsView!: GRIN2ResultsView\n\tprivate controlsView: GRIN2ControlsView | null = null\n\tprivate controlsToggleButton: any = null\n\tprivate hasResults = false\n\tprivate inputPanelCollapsed = false\n\tprivate cohortFilterSignature: string | null = null\n\n\tconstructor(opts: any, api) {\n\t\tsuper(opts, api)\n\t\tthis.opts = opts\n\t\tthis.components = { controls: {} as ComponentApi }\n\t\topts.holder.classed('sjpp-grin2-main', true)\n\t\tconst massControls = opts.holder.append('div').style('display', 'inline-block')\n\t\tconst inputPanel = opts.holder\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-grin2-input-panel')\n\t\t\t.style('display', 'grid')\n\t\t\t.style('grid-template-rows', '1fr')\n\t\t\t.style('opacity', '1')\n\t\t\t.style('transition', 'grid-template-rows 250ms ease, opacity 200ms ease')\n\t\tconst inputPanelContent = inputPanel.append('div').style('min-height', '0').style('overflow', 'hidden')\n\t\tthis.dom = {\n\t\t\tmassControls,\n\t\t\tinputPanel,\n\t\t\theaderText: inputPanelContent.append('div').style('display', 'inline-block'),\n\t\t\tcontrols: inputPanelContent.append('div'),\n\t\t\tcontrolsToggle: opts.holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('align-items', 'center')\n\t\t\t\t.style('gap', '8px')\n\t\t\t\t.style('margin', '10px 20px 10px 100px'),\n\t\t\tdiv: opts.holder.append('div').style('margin', '20px')\n\t\t}\n\t\tif (opts.header) this.dom.header = opts.header.text('GRIN2')\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\tconst parentConfig = appState.plots.find((p: BasePlotConfig) => p.id === this.parentId)\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn { config, termfilter }\n\t}\n\n\tasync init() {\n\t\tthis.model = new GRIN2Model(this.app.vocabApi)\n\t\tthis.resultsView = new GRIN2ResultsView(this.dom.div, this.app)\n\t\tthis.controlsToggleButton = this.dom.controlsToggle\n\t\t\t.append('button')\n\t\t\t.attr('type', 'button')\n\t\t\t.attr('data-testid', 'sjpp-grin2-input-toggle')\n\t\t\t.style('display', 'none')\n\t\t\t.on('click', () => {\n\t\t\t\tif (!this.hasResults) return\n\t\t\t\tthis.inputPanelCollapsed = !this.inputPanelCollapsed\n\t\t\t\tthis.updateInputPanel()\n\t\t\t})\n\t\tthis.updateInputPanel()\n\t\tthis.components.controls = await controlsInit({\n\t\t\tapp: this.app,\n\t\t\tid: this.id,\n\t\t\tholder: this.dom.massControls.style('display', 'inline-block'),\n\t\t\tinputs: []\n\t\t})\n\n\t\t// Remove the burger and download buttons for now\n\t\tconst burgerMenu = this.dom.massControls.select('div > svg.bi.bi-copy')\n\t\tif (burgerMenu) burgerMenu.remove()\n\t\tconst downloadBtn = this.dom.massControls.select('div > svg.bi.bi-download')\n\t\tif (downloadBtn) downloadBtn.remove()\n\n\t\tthis.components.controls.on('helpClick.grin2', () => {\n\t\t\twindow.open('https://github.com/stjude/proteinpaint/wiki/Grin2')\n\t\t})\n\t}\n\n\tasync main() {\n\t\tconst config = structuredClone(this.state.config)\n\t\tif (config.childType != this.type && config.chartType != this.type) return\n\n\t\tconst cohortFilterSignature = this.getCohortFilterSignature()\n\t\tif (this.cohortFilterSignature === null) {\n\t\t\tthis.cohortFilterSignature = cohortFilterSignature\n\t\t} else if (this.cohortFilterSignature !== cohortFilterSignature) {\n\t\t\tthis.cohortFilterSignature = cohortFilterSignature\n\t\t\tthis.clearResultsAndShowInputs()\n\t\t}\n\n\t\tif (!this.controlsView) {\n\t\t\tthis.controlsView = new GRIN2ControlsView({\n\t\t\t\theaderHolder: this.dom.headerText,\n\t\t\t\tcontrolsHolder: this.dom.controls,\n\t\t\t\tconfig: this.state.config,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tgenome: this.app.opts.genome,\n\t\t\t\tactionsHolder: this.dom.controlsToggle,\n\t\t\t\tcallbacks: { onRun: () => this.handleRun() }\n\t\t\t})\n\t\t\tthis.controlsView.build()\n\t\t\tif (this.state.config.settings.runAnalysis) this.handleRun()\n\t\t}\n\t}\n\n\tprivate async handleRun() {\n\t\tif (!this.controlsView) return\n\t\tconst runFilterSignature = this.cohortFilterSignature\n\t\t// The previous result is removed before a new request starts, so its input toggle must disappear too.\n\t\t// Keeping the panel open also makes errors recoverable without another click.\n\t\tthis.clearResultsAndShowInputs()\n\t\tthis.controlsView.setBusy(true)\n\t\ttry {\n\t\t\tconst dtUsage = this.controlsView.getDtUsage()\n\n\t\t\tconst configValues = this.controlsView.getConfigValues(dtUsage)\n\t\t\tconst manhattan = this.state.config.settings.manhattan\n\t\t\tconst requestData = {\n\t\t\t\tfilter: getNormalRoot(this.state.termfilter.filter),\n\t\t\t\tfilter0: this.state.termfilter.filter0,\n\t\t\t\twidth: manhattan?.plotWidth,\n\t\t\t\theight: manhattan?.plotHeight,\n\t\t\t\tpngDotRadius: manhattan?.pngDotRadius,\n\t\t\t\tdevicePixelRatio: window.devicePixelRatio,\n\t\t\t\tmaxGenesToShow: manhattan?.maxGenesToShow,\n\t\t\t\tlesionTypeColors: manhattan?.lesionTypeColors,\n\t\t\t\tqValueThreshold: manhattan?.qValueThreshold,\n\t\t\t\tmaxCappedPoints: manhattan?.maxCappedPoints,\n\t\t\t\thardCap: manhattan?.hardCap,\n\t\t\t\tbinSize: manhattan?.binSize,\n\t\t\t\t...configValues\n\t\t\t}\n\n\t\t\tconst response = await this.model.fetchGrin2Data(requestData, this.api!.getAbortSignal())\n\t\t\tif (response.status === 'error') throw `GRIN2 analysis failed: ${response.error}`\n\t\t\t// A filter update invalidates this response even if the request could not be aborted in time.\n\t\t\tif (runFilterSignature !== this.cohortFilterSignature) return\n\n\t\t\tconst vm = new GRIN2ViewModel(response, manhattan, dtUsage)\n\t\t\tthis.resultsView.render(vm.viewData)\n\t\t\tthis.hasResults = true\n\t\t\tthis.inputPanelCollapsed = true\n\t\t\tthis.updateInputPanel()\n\n\t\t\tthis.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: this.id,\n\t\t\t\tconfig: {\n\t\t\t\t\t...this.state.config,\n\t\t\t\t\tsettings: {\n\t\t\t\t\t\t...this.state.config.settings,\n\t\t\t\t\t\t...configValues,\n\t\t\t\t\t\tdtUsage,\n\t\t\t\t\t\trunAnalysis: true\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t} catch (error) {\n\t\t\t// Component updates abort the previous request; this is expected during filter changes.\n\t\t\tif (this.app.isAbortError(error)) return\n\t\t\t// dom.div may be undefined if the sandbox was deleted mid-request \u2014 don't crash in that case\n\t\t\tif (this.dom.div) {\n\t\t\t\tsayerror(this.dom.div, `Error running GRIN2: ${error instanceof Error ? error.message : error}`)\n\t\t\t}\n\t\t} finally {\n\t\t\tthis.controlsView?.setBusy(false)\n\t\t}\n\t}\n\n\tprivate getCohortFilterSignature() {\n\t\treturn JSON.stringify({\n\t\t\tfilter: this.state.termfilter?.filter ?? null,\n\t\t\tfilter0: this.state.termfilter?.filter0 ?? null\n\t\t})\n\t}\n\n\tprivate clearResultsAndShowInputs() {\n\t\tthis.resultsView.clear()\n\t\tthis.hasResults = false\n\t\tthis.inputPanelCollapsed = false\n\t\tthis.updateInputPanel()\n\t}\n\n\tprivate updateInputPanel() {\n\t\tthis.dom.inputPanel\n\t\t\t.attr('aria-hidden', String(this.inputPanelCollapsed))\n\t\t\t.property('inert', this.inputPanelCollapsed)\n\t\t\t.style('grid-template-rows', this.inputPanelCollapsed ? '0fr' : '1fr')\n\t\t\t.style('opacity', this.inputPanelCollapsed ? '0' : '1')\n\t\t\t.style('pointer-events', this.inputPanelCollapsed ? 'none' : 'auto')\n\t\tthis.controlsToggleButton?.style('display', this.hasResults ? null : 'none')\n\t\tthis.dom.controlsToggle\n\t\t\t.select('[data-testid=\"sjpp-grin2-run-button\"]')\n\t\t\t.style('display', this.inputPanelCollapsed ? 'none' : null)\n\t\tthis.controlsToggleButton\n\t\t\t?.attr('aria-expanded', String(!this.inputPanelCollapsed))\n\t\t\t.text(this.inputPanelCollapsed ? 'Show input options' : 'Hide input options')\n\t}\n}\n\nexport const grin2Init = getCompInit(GRIN2)\nexport const componentInit = grin2Init\n\nexport async function getPlotConfig(opts: GRIN2Opts, app: MassAppApi) {\n\tconst queries = app.vocabApi.termdbConfig.queries\n\tconst defaultSettings = getDefaultGRIN2Settings(opts)\n\n\tconst dtUsage: any = {}\n\n\t// Dynamically add data type options based on availability\n\tif (queries?.snvindel) {\n\t\tdtUsage[dtsnvindel] = { checked: true, label: dt2lesion[dtsnvindel].uilabel }\n\t}\n\t// CNV is available either via a ds-level cnv query (file-based ds) or via per-sample cnv file types\n\t// declared on singleSampleMutation (e.g. GDC, which has no queries.cnv but serves cnv per case).\n\tif (queries?.cnv || queries?.singleSampleMutation?.cnvTypes?.length) {\n\t\tdtUsage[dtcnv] = { checked: true, label: dt2lesion[dtcnv].uilabel }\n\t}\n\tif (queries?.svfusion) {\n\t\tif (queries.svfusion.dtLst.includes(dtfusionrna)) {\n\t\t\tdtUsage[dtfusionrna] = { checked: false, label: dt2lesion[dtfusionrna].uilabel }\n\t\t}\n\t\tif (queries.svfusion.dtLst.includes(dtsv)) {\n\t\t\tdtUsage[dtsv] = { checked: false, label: dt2lesion[dtsv].uilabel }\n\t\t}\n\t}\n\tif (queries?.itd) {\n\t\tdtUsage[dtitd] = { checked: false, label: dt2lesion[dtitd].uilabel }\n\t}\n\n\t// snvindelOptions / cnvOptions / fusionOptions / svOptions are intentionally not seeded here.\n\t// ControlsView supplies the user-visible defaults via its own fallback chain\n\t// (savedCnv ?? dsConfig ?? CNV_*_FALLBACK), and handleRun writes the live form values\n\t// back into settings on each Run. So before the first Run these stay undefined; after,\n\t// they are always present from the form. Seeding them here would only add magic numbers\n\t// that no code reads.\n\tconst config = {\n\t\tchartType: 'grin2',\n\t\tsettings: {\n\t\t\tcontrols: {},\n\t\t\tdtUsage,\n\t\t\trunAnalysis: false,\n\t\t\tmanhattan: {\n\t\t\t\t...defaultSettings.manhattan,\n\t\t\t\t...opts?.manhattan\n\t\t\t}\n\t\t}\n\t}\n\n\treturn copyMerge(config, opts)\n}\n"],
+  "mappings": 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+  "names": []
+}

package/dist/hierCluster-QFPRMHVA.js

@@ -0,0 +1,63 @@
+import {
+  HierCluster,
+  componentInit,
+  hierClusterInit
+} from "./chunk-WFCSOTBO.js";
+import {
+  getPlotConfig
+} from "./chunk-WZ2L57MB.js";
+import "./chunk-G5S4R77D.js";
+import "./chunk-G764NXQN.js";
+import "./chunk-ESGXULRH.js";
+import "./chunk-T25QNZHB.js";
+import "./chunk-W3WPPOXH.js";
+import "./chunk-OXVLWQ6M.js";
+import "./chunk-2MG6XE6R.js";
+import "./chunk-L7IRWUKT.js";
+import "./chunk-HUBO743S.js";
+import "./chunk-BHGISFCA.js";
+import "./chunk-ONPKE6DC.js";
+import "./chunk-DDKS3MV3.js";
+import "./chunk-UGRQXBL4.js";
+import "./chunk-CDD7LYJM.js";
+import "./chunk-YQBS2ZCK.js";
+import "./chunk-RKO6BL5N.js";
+import "./chunk-V2OJLJSK.js";
+import "./chunk-5VOPABBA.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-Z5U6HOE4.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-5ABGFJSP.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-XPY6AWXO.js";
+import "./chunk-NELOT3NJ.js";
+import "./chunk-M6EF3WVV.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-LFCYMSVA.js";
+import "./chunk-I6WR4CG7.js";
+import "./chunk-2X6W4E3W.js";
+import "./chunk-NYRZNRG5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-3XVVN66M.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-NSTL4MY2.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  HierCluster,
+  componentInit,
+  getPlotConfig,
+  hierClusterInit
+};
+//# sourceMappingURL=hierCluster-QFPRMHVA.js.map

package/dist/hierCluster-YWC3XYPV.js

@@ -0,0 +1,59 @@
+import {
+  HierCluster,
+  componentInit,
+  hierClusterInit
+} from "./chunk-WFCSOTBO.js";
+import "./chunk-G5S4R77D.js";
+import "./chunk-G764NXQN.js";
+import "./chunk-ESGXULRH.js";
+import "./chunk-T25QNZHB.js";
+import "./chunk-W3WPPOXH.js";
+import "./chunk-OXVLWQ6M.js";
+import "./chunk-2MG6XE6R.js";
+import "./chunk-L7IRWUKT.js";
+import "./chunk-HUBO743S.js";
+import "./chunk-BHGISFCA.js";
+import "./chunk-ONPKE6DC.js";
+import "./chunk-DDKS3MV3.js";
+import "./chunk-UGRQXBL4.js";
+import "./chunk-CDD7LYJM.js";
+import "./chunk-YQBS2ZCK.js";
+import "./chunk-RKO6BL5N.js";
+import "./chunk-V2OJLJSK.js";
+import "./chunk-5VOPABBA.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-Z5U6HOE4.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-5ABGFJSP.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-XPY6AWXO.js";
+import "./chunk-NELOT3NJ.js";
+import "./chunk-M6EF3WVV.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-LFCYMSVA.js";
+import "./chunk-I6WR4CG7.js";
+import "./chunk-2X6W4E3W.js";
+import "./chunk-NYRZNRG5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-3XVVN66M.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-NSTL4MY2.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  HierCluster,
+  componentInit,
+  hierClusterInit
+};
+//# sourceMappingURL=hierCluster-YWC3XYPV.js.map

package/dist/hierCluster.config-F7YYZNM3.js

@@ -0,0 +1,40 @@
+import {
+  getPlotConfig
+} from "./chunk-WZ2L57MB.js";
+import "./chunk-W3WPPOXH.js";
+import "./chunk-OXVLWQ6M.js";
+import "./chunk-5VOPABBA.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-Z5U6HOE4.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-5ABGFJSP.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-XPY6AWXO.js";
+import "./chunk-NELOT3NJ.js";
+import "./chunk-M6EF3WVV.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-LFCYMSVA.js";
+import "./chunk-I6WR4CG7.js";
+import "./chunk-2X6W4E3W.js";
+import "./chunk-NYRZNRG5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-3XVVN66M.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-NSTL4MY2.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  getPlotConfig
+};
+//# sourceMappingURL=hierCluster.config-F7YYZNM3.js.map